Hi BioC-support,

I thought that I share here the announcement I made on Twitter about our recent work that was submitted to Bioconductor.

Best, Leo

🔥off the press! Check 👀 our @biorxivpreprint on human 🧠brain @LieberInstitute spatial 🗺️🔬transcriptomics data 🧬using Visium @10xGenomics 🎉 #spatialLIBD

🔍http://spatial.libd.org/spatialLIBD/ 👩🏾‍💻https://github.com/LieberInstitute/HumanPilot 📚http://research.libd.org/spatialLIBD/ 📦https://github.com/LieberInstitute/spatialLIBD

https://www.biorxiv.org/content/10.1101/2020.02.28.969931v1

Our study shows 12 samples from 3 human brain DLPFC neuronal layers + white matter with @10xGenomics's Visium platform. Features 📜:

• Largest so far
• Harder to cluster than the example mouse data
• Data is all public
• @Bioconductor #rstats 📦
• #shiny web app
• Assessment of known markers
• Identification of layer-specific markers
• smFISH validation ✅
• spatial registration of snRNA-seq data
• Layer-enrichment of neurodevelopmental and neuropsychiatric gene sets
• Data-driven layer-enriched clustering in the DLPFC

This was a great collaboration between @LieberInstitute @jhubiostat @10xGenomics and in particular by @krmaynard @lmwebr @sudoBreeB @mattntran https://linkedin.com/in/nikhil-rao-phd-pmp-a1422614/ @stephaniehicks @martinowk @andrewejaffe

It was a pleasure to be involved in this project!

And if you want to jump in 🤿 and access the data, you can through spatialLIBD::fetch_data() (currently under review at @bioconductor: https://github.com/Bioconductor/Contributions/issues/1389) or download the h5, image and loupe files

http://research.libd.org/spatialLIBD/

And we'd love to talk to you, hear your feedback, collaborate 🤝and/or hire 👩🏾‍💻👨🏾‍🔬you. Find us at:

• March 19 https://the-scientist.com
• March 26-27

  Please RT! CVCSN 2020 "The Neuroscience of Disease" in #Blacksburg #VA March 26-27 @VT_Science @vtcsom @BEAMvt @VTresearch pic.twitter.com/TIDPZWgQOG

  — VirginiaNeuroscience (@VirginiaNeuro) January 6, 2020

• March 30 @LIIGH_UNAM
• April 2020 Single Cell Symp
• May #BoG2020 @cshlmeetings
• May @erum2020_conf
• July #BioC2020 @Bioconductor

To close off my 7-layered tweet ;) I wrote a blog post about "Diving together into the unknown world of spatial transcriptomics" http://lcolladotor.github.io/2020/02/29/diving-together-into-the-unknown-world-of-spatial-transcriptomics/

spatialLIBD #stats #scicomm #IntoTheUnknown #Bioconductor #OpenScience

For more, check

🔥off the press! 👀 our @biorxivpreprint on human 🧠brain @LieberInstitute spatial 🌌🔬transcriptomics data 🧬using Visium @10xGenomics🎉#spatialLIBD

🔍https://t.co/RTW0VscUKR
👩🏾‍💻https://t.co/bsg04XKONr
📚https://t.co/FJDOOzrAJ6
📦https://t.co/Au5jwADGhYhttps://t.co/PiWEDN9q2N pic.twitter.com/aWy0yLlR50

— 🇲🇽 Dr. Leonardo Collado-Torres (@fellgernon) February 29, 2020